New York state came up $200 million short of its payroll-tax projection for 2009 — and that could lead to MTA service cuts as early as next year, sources said yesterday.

But there won’t be a fare hike in 2010, not with one already scheduled for 2011, MTA officials noted.

“If fares are off the table, I don’t know how else to rescue the budget by that much money without service cuts, as well as additional administrative savings,” one board member said.

Since Gov. Paterson cut $143 million from its budget this year, the MTA has to make up $343 million by the end of next year.